Gut microbiome in melanoma patients, New York, longitudinal
48 stool samples from melanoma patients in New York (mostly elderly and adult, with some infant) undergoing immunotherapy, examined in a longitudinal design relating pre-treatment gut microbiome to progression-free survival. machine-written summary
48 samples · 48 runs · US · Elderly · 2019 · 4.59 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 755 sample values (age, antibiotic exposure, bmi, collection date, country, health condition, health condition detail, intervention) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 48 sample values (location site) · PMC10246505, PMC10654443, PMC10957474, PMC11560503, PMC11783787, PMC11879847, PMC11937697, PMC12402269, PMC12475161, PMC12654497, PMC13388844, PMC13584529, PMC6785875, PMC7664509, PMC7714408, PMC8513370, PMC8938272, PMC9053858, PMC9295706, PMC9925043 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: two sequence archives disagree for 3 samples (e.g. 54.3 vs 19832.1) — withheld; antibiotic exposure: sequence archive and curatedMetagenomicData disagree for 10 samples (e.g. yes vs no) — withheld.
The sources disagree on 12 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (13)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN11605819 | age | 54.3 (sequence archive) | 19832.1 (sequence archive) | withheld: neither value published |
| SAMN11605820 | age | 54.3 (sequence archive) | 19832.1 (sequence archive) | withheld: neither value published |
| SAMN11605837 | age | 54.3 (sequence archive) | 19723.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11605812 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN11605821 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN11605833 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN11605837 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN11605838 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN11605842 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN11605844 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN11605845 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN11605849 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN11605853 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
longitudinal — not resolved
Schedule stated by the source: “Stool collected at baseline (pre-treatment), 6 weeks, and 12 weeks after immunotherapy start” (time origin: intervention start); stated follow-up 3 mo.
Genera, mean relative abundance over 40 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 48 | 100% | ||||
| country | 48 | 100% | 48 | |||
| health_condition | 48 | 100% | 48 | |||
| subject_id | 0 | 0% | ||||
| bmi | 48 | 100% | 48 | |||
| collection_date | 48 | 100% | 48 | |||
| detailed_location | 48 | 100% | ||||
| health_condition_detail | 48 | 100% | 48 | |||
| intervention | 48 | 100% | 48 | |||
| intervention_detail | 48 | 100% | 48 | |||
| latitude | 48 | 100% | 48 | |||
| location_region | 48 | 100% | 48 | |||
| location_site | 48 | 100% | 48 | |||
| longitude | 48 | 100% | 48 | |||
| medication | 48 | 100% | 48 | |||
| medication_detail | 48 | 100% | 48 | |||
| sex | 48 | 100% | 48 | |||
| timepoint_label | 48 | 100% | 48 | |||
| age_at_collection_days | 45 | 94% | 45 | |||
| antibiotic_exposure | 38 | 79% | 38 |
- Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients. 2019 PMID 31597568 PMC6785875 own_data
- Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma. 2021 PMID 34641962 PMC8513370 own_data
- Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers. 2021 PMID 33175106 PMC7664509 unsure
- Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma. 2020 PMID 33268597 PMC7714408 unsure
- A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors. 2021 PMID 33593881 PMC9053858 unsure
15 more
- Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. 2022 PMID 35228751 PMC8938272
- Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1. 2022 PMID 35228752 PMC10246505
- Predicting cancer immunotherapy response from gut microbiomes using machine learning models. 2022 PMID 35875611 PMC9295706
- The microbiome-derived metabolite TMAO drives immune activation and boosts responses to immune checkpoint blockade in pancreatic cancer. 2022 PMID 36083892 PMC9925043
- Gut microbial structural variation associates with immune checkpoint inhibitor response. 2023 PMID 37973916 PMC10654443
- Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma. 2024 PMID 38365950 PMC10957474
- Neoadjuvant vidutolimod and nivolumab in high-risk resectable melanoma: A prospective phase II trial. 2024 PMID 39486411 PMC11560503
- MiCML: a causal machine learning cloud platform for the analysis of treatment effects using microbiome profiles. 2025 PMID 39885552 PMC11783787
- Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses. 2025 PMID 39929976 PMC11879847
- Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types. 2025 PMID 40151642 PMC11937697
- Microbiome data integration via shared dictionary learning. 2025 PMID 40890119 PMC12402269
- Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis. 2025 PMID 41006325 PMC12475161
- Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts. 2025 PMID 41304278 PMC12654497
- Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis. 2026 PMID 42189287 PMC13388844
- Decoding the cancer microbiome: multi-omics, AI, and translational opportunities. 2026 PMID 42750046 PMC13584529
Archive description
Our goal was to characterize whether the pre-therapy gut microbiome is related to immunotherapy responses in melanoma patients
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly and adult by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Gut microbiome in melanoma patients”
- life stage sample.attr.age · “60.77255 (n=36/48)”
- life stage sample.attr.age · “54.2698 (n=12/48)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11605812 | age_at_collection_days | 22197.2 | R1 | 0.70 | sample.attr.age | 60.77255 |
| SAMN11605813 | antibiotic_exposure | yes | R1 | 0.70 | sample.attr.antibio_flag_6mo | 1 |
| SAMN11605812 | bmi | 20.75 | R1 | 0.90 | sample.attr.bmi | 20.75 |
| SAMN11605812 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN11605812 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: New York |
| SAMN11605812 | health_condition | other_cancer | R1 | 0.85 | biosample.attribute:stage | III |
| SAMN11605812 | health_condition_detail | III | R1 | 0.85 | biosample.attribute:stage | III |
| SAMN11605812 | intervention | drug_therapy | R1 | 0.80 | biosample.attribute:immunotherapy | immunotherapy: CTLA4/PD1 |
| SAMN11605812 | intervention_detail | combined anti-CTLA-4 plus anti-PD-1 immunotherapy | R1 | 0.80 | biosample.attribute:immunotherapy | immunotherapy: CTLA4/PD1 |
| SAMN11605812 | latitude | 40.7423 | R1 | 0.90 | biosample.attribute:lat_lon | 40.742344 N 73.974533 W |
| SAMN11605812 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: New York |
| SAMN11605812 | location_site | NYU Langone Health | R3 | 0.70 | paper.fulltext.methods | scheduled to receive immunotherapy at NYU Langone Health |
| SAMN11605812 | longitude | -73.9745 | R1 | 0.90 | biosample.attribute:lat_lon | 40.742344 N 73.974533 W |
| SAMN11605812 | medication | immunosuppressant_or_biologic | R1 | 0.85 | biosample.attribute:immunotherapy | CTLA4/PD1 |
| SAMN11605812 | medication_detail | CTLA4/PD1 | R1 | 0.85 | biosample.attribute:immunotherapy | CTLA4/PD1 |
| SAMN11605812 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN11605812 | timepoint_label | Baseline | R1 | 0.85 | sample.attr.time | Baseline |
Sequencing
48 runs over 48 samples · mean 6.94 Gbp per run (median 4.59 Gbp, total 333.07 Gbp; 48 runs with a base count) · layout PAIRED 48 · platform ILLUMINA 48 · models Illumina HiSeq 2500 (48) · 83% of runs with a Sandpiper profile · first public 2019-09-10
Authors (68)
Sardar P first · Beresford-Jones BS · Xia W · Shabana O · Suyama S · Ramos RJF · Soderholm AT · Tourlomousis P · Kuo P · Evans AC · Imianowski CJ · Conti AG · Wesolowski AJ · Baker NM · McCord EAL · Okkenhaug K · Whiteside SK · Roychoudhuri R · Bryant CE · Cross JR · Pedicord VA last · Zhang L first · Zhou DD · Feng J · Liao ZJ · Shu XL · Yang RM · Gao YC · Zhou HH · Zhang W · Zou Y · Liu R last · Qiao T first · Zhu Z last · Huang S first · Chaudhari DS · Shukla R · Kanani P · Zeidan RS · Lin Y · Burrow W · Mankowski RT · Jain S · Yadav H last · Candeliere F first · Busi E · Cerri S · Sola L · Lombardi M · Greco S · Pedroni S · Amaretti A · Raimondi S · Chiavelli C · Vitale MG · Bertolini F · Depenni R · Franchini G · Dominici M · Rossi M last · Sun Y first · Cheng OJ · Ma A · Shabnaz S · Huang X · Zhao J · Tan AC · Ma Q last
Downloads
PRJNA541981.csv.gz (2.8 KB) · parquet (74.2 KB) — all 48 samples, every field with route and confidence · PRJNA541981_determinations.csv.gz (6.3 KB) — 803 evidence rows